147141ee5432ca1fc3e06bad3da5c9c0 *DESCRIPTION
699e9f2656fa26e50411dca8264764a6 *NAMESPACE
29437d98ffa268c073a9ce72cedad350 *R/Pillai.R
17f848a9c25149fca00a59c940f61ba5 *R/Rcpp_exceptions.R
02594621534b024fec0425bd74ccc1a5 *R/addExtraMarkerFromRawCall.R
079adb7b7d5ea7f9ea57bef8e8496d8e *R/addExtraMarkers.R
2990a060f51ed09ba216d9c82c2afc85 *R/additionOperators.R
001c49700c65bf11df1806a494e2a7ad *R/as.mpInterval.R
d09ff1d04360b04ef757a4fe6c2da14a *R/assignFounderPattern.R
a9834304cf847ab69c0879a7352258a4 *R/assignFounderPatternPrototype.R
7dd0c6f1e32584e63c17a5fe24b81649 *R/backcrossPedigree.R
90f1047abd665c9264a3569c19ea2579 *R/biparentalDominant.R
72b74eaa85676b556b9c9e33390b67a7 *R/callFromMap.R
327612d264502e6968583f9d06a64f16 *R/canSkipValidity.R
baaaf2b1d80b8deb3125998b9b7749e0 *R/changeMarkerPosition.R
cdac814fe60c21bc3239bbdcbb067dce *R/combineGenotypes.R
b2ca40c4bb3ba47307c0af92c756331d *R/combineKeepRF.R
46a192c13866b3eca773eea09bef484f *R/compressedProbabilities.R
e75330832528400599ea3ccd45b6d169 *R/computeAllEpistaticChiSquared.R
c78660543e351092ca6e31afcd49f7de *R/computeGenotypeProbabilities.R
4891beb7c010d268e4aae24a5f8a7182 *R/createSNPTemplate.R
bd79f722e6ce703c0f57e28d93c3d9a0 *R/detailedPedigree-class.R
08b52906a577ce5871554378170ff84e *R/eightWayPedigreeImproperFunnels.R
f623b89e5bbadd7b2aa1ce0042128bd1 *R/eightWayPedigreeRandomFunnels.R
661ff6eabb4c682bf6d43699143e0243 *R/eightWayPedigreeSingleFunnel.R
ae512e7e5201c75ade36410d8693f569 *R/estimateMap.R
73fe9e723447692bbbb82abf51cf2bec *R/estimateMapFromImputation.R
af014a58c5e66a0f0e6f138ee2d61e75 *R/estimateRF.R
76cff94b467bdc982a52be1ba932e3d0 *R/estimateRFSingleDesign.R
c58d2586c4c209c4b200203055f06101 *R/expand.R
5067c4efe25218fb330bd3b95d781bfb *R/expandedProbabilities.R
dafd582e7525486a27bdbe1425b20b1e *R/exportMapToPretzl.R
7c39aae7cb599296edeae1a6abf14426 *R/extraImputationPoints.R
1e46493258d00867a4728930536f7eff *R/f2Pedigree.R
3711b1a7b930d5e8a7a7250b97ea4214 *R/finals.R
158d71259b964fbd10fafeab36ad8420 *R/fixedNumberOfFounderAlleles.R
5aff43b8fa9fcce4c27a98fdcc2ecd9a *R/formGroups.R
b0c7c3fd1f3477f069c8af5c7683ab40 *R/founders.R
d050051808c11a43de924b2422e372f8 *R/fourParentPedigreeRandomFunnels.R
af1d79ba05b7955ca4db122d116ecdd0 *R/fourParentPedigreeSingleFunnel.R
b72e179e7077cf4b8e5cfd4822036ccc *R/fullHetData.R
50041e68f4a91547543fb7c0ca6de252 *R/generateGridPositions.R
9e18b6f79a4695a298a87e11bfdca864 *R/generateIntervalMidPoints.R
4eadd3a5db3f538bf2842873792f328d *R/geneticData-class.R
35346c1f9f695481f067f7decb02f035 *R/getAllFunnels.R
7516404593d7c7571a849520c82675d0 *R/getChromosomes.R
eabc4fc6595a24c8b39dfca734301623 *R/getIntercrossingAndSelfingGenerations.R
cddabf299aeb95a5106a5981140f3ef9 *R/getPositions.R
af0ce61fc6b07cebbdc28421400d8884 *R/hetData-class.R
dae0c1fae76dccf06ad76f639f518e9f *R/hetData.R
22983cb1965b39848dcbd34f8e219e37 *R/identC.R
ffb21c283e19bc800434a6d5f447204b *R/imputationGenerics.R
0505acdd52eafd0b2ba01b54256262f0 *R/impute.R
2f34a812b5d36d819208f7254fe13345 *R/imputeFounders.R
de55aedb1fec133e0c70e4ff1a1c10a8 *R/jitterMap.R
febd38fc247c703689e18e6027678c1d *R/lg-class.R
687fd4a7f6c70aea5913a0683c393e56 *R/lineNames.R
2d64fe71d78d36fb45e32c8cc151e048 *R/listCodingErrors.R
f760017a15aaa5462257db16bef174e7 *R/map-class.R
baecaf3d6815738b2a62956d30585a25 *R/mapFunctions.R
da078481e3a5426f28e30f170a9df8be *R/markers.R
9a209179570120da631a9c51837172af *R/mpcross-class.R
31882ba33a096f1754e0a7e0d87ae778 *R/mpcross.R
24070a18d6b2b435b27e73dd3ae730c8 *R/multiparentSNP.R
c9dc0924b6877bf20791802a4c399d3f *R/multiparentSNPPrototype.R
3194fa14e04884d97828fb329730b6e1 *R/nFounders.R
b810231c90c7a8d17063dde5189cd6db *R/nLines.R
6093c815b381f867049ea6abd4b92d2e *R/nMarkers.R
7d55d0015add40e7efa2cfbf21d4792e *R/num_threads.R
e81a68325ee8b600fdb0f554efacfeea *R/orderCross.R
7087fdb2572c151e1c422e38b5b50475 *R/pedigree-class.R
69adf321073a8b587f3db41a96244354 *R/pedigree.R
49408b2e43a0ec37e0d1dc0674592245 *R/pedigreeGraph-class.R
e416ab57ace996bba9d33753862a66cb *R/pedigreeGraph.R
60247d6acc4d5937d2f5b5ea9ee6e3e2 *R/pedigreeToGraph.R
f3d51d3b35743f054ac2cc5f5342c656 *R/plot.R
2937801e7d2b5532d568fccef5ee7ec6 *R/plotMosaic.R
6cce7fbc05fb31a1bd0db3bcf1e2f291 *R/plotProbabilities.R
a12c78aa23eae38f206cc3e84a46aa10 *R/print.R
54adfeb4bc1d88002621dfe11517341d *R/probabilityData.R
f327bf33c3902b686039087646bbcae8 *R/purdyToPedigree.R
74dc6711caa5ac1269b4d10e41d35fe7 *R/rawSymmetricMatrix.R
ea8cdee76aac8158354c71e831300b56 *R/redact.R
5bbe0e89fe45527473cc4afa0c51ab61 *R/removeHets.R
bdb2b4577c03ad938a552090d54b2914 *R/reorderPedigree.R
31119abd3808b7c4f9ec7ed6e213d229 *R/reverseChromosomes.R
651b86bc0f79e6ac4d44a8cfdfef5a05 *R/rf-class.R
3eb56c0831317a0a4b26941c5f255dcf *R/rilPedigree.R
1c714e64c8e902302666204b937123b1 *R/roxygen.R
681594a8426b2b46d61325013bc2c29e *R/selfing.R
782ebc6db2c583247ffe64ba14ecf598 *R/show.R
4aab24ef8961e670e9ce81c261bdfc00 *R/simulateMPCross.R
5bd0add2c4546a45e0f1eabf63929eeb *R/simulatePhenotypes.R
13e7999cd25c21842136681bc3694da8 *R/singleLocusProbabilities.R
4e7ea672304ade40d506869e3e46660b *R/sixteenParentPedigreeRandomFunnels.R
3d643fa492f2256e9406244db591ada2 *R/stripPedigree.R
3ca49e54b34502805f37febab952a0d0 *R/subset.R
1a4e9e8ab42cc404889712168203c426 *R/testDistortion.R
8427f59419632a02d55f11aa18ab1719 *R/toMpMap.R
3decd9ac4382231e8c60780595b11c1f *R/transposeProbabilities.R
71c4fb5638d7579eb7802367bf821f2c *R/twoParentPedigree.R
6dd243c19ee960120274c2a0b0799082 *R/validation.R
51a08bac058c73a0ee0a912fdd6ac396 *README.md
b9f289924256e8ed96c696e7c1f85471 *build/vignette.rds
3e1711ff0219e0a76c78eb0915295dde *data/callFromMapExampleLocalisationStatistics.RData
14cecad04183f6b35d87ac0c07ced250 *data/eightParentSubsetMap.RData
20d33cbb13ca11ef2cba04cf29a95b9c *data/simulatedFourParentData.RData
cb14c638b1808fbb34e518461a53a1d6 *data/wsnp_Ku_rep_c103074_89904851.RData
6803f89a860e304518ce283032bb917f *inst/doc/mpMap2.R
6a53c4d147a635370403b2b5931d3d33 *inst/doc/mpMap2.Rnw
ca62f3b7486ced93225f38c16b14bc05 *inst/doc/mpMap2.pdf
f31584b418c8f31ec8efe20c8eb6af2a *inst/generateDatasets/generateExample1.R
edd6d59d5e176e57cc4e09c13f160711 *inst/mathematica/finiteSelfingIntercrossing16Way.nb
961ab9788a668f1b178d9a0d1798d2cc *inst/mathematica/finiteSelfingIntercrossing16Way.states
3dad34c4a3b0b603194af5167fe47eec *inst/mathematica/finiteSelfingIntercrossing4Way.nb
1db6297a0f6f4d26a13be4a1dedb87b7 *inst/mathematica/finiteSelfingIntercrossing4WaySingleFunnel.nb
13ab8991ffe13f60344a636537670b6b *inst/mathematica/finiteSelfingIntercrossing8Way.nb
5c2d519153ed3d62c656648e4ca3f471 *inst/mathematica/finiteSelfingIntercrossing8WaySingleFunnel.nb
19d29d80c981d3cc456b33e861247779 *inst/mathematica/finiteSelfingIntercrossing8WaySinglePoint.nb
4351690e97faabe503f71bdd67c97e41 *inst/mathematica/finiteSelfingIntercrossingF2.nb
f071c80d3f2169df4aebc90998b223a7 *man/addExtraMarkerFromRawCall.Rd
56f50785f73a8cbb399ff89c8546bb7e *man/addExtraMarkers.Rd
27eba52c8875f28911d42070978e1c6f *man/as.mpInterval.Rd
39702f0ed17d8e8abe992a94be60480c *man/assignFounderPattern.Rd
7c12437bde2512da1e7b7caf23e1ecbb *man/backcrossPedigree.Rd
3193134e801244b8e0f70c714b263969 *man/biparentalDominant.Rd
12d81ba5484619561ffd4d65b552c87d *man/callFromMap.Rd
6fdaa1123f79b65a4ffacb6f6ef11609 *man/changeMarkerPosition.Rd
a2109a9529780ce64b08c459b4ee0050 *man/clusterOrderCross.Rd
e67358c25dbf0e214957cabce0faa976 *man/combineKeepRF.Rd
a6f8fa64a6ba112a3d97a86ab0b81118 *man/combineMpcross.Rd
d2e009262a5c77c3e712a87c795af7eb *man/computeAllEpistaticChiSquared.Rd
785920c71fad25089d4ca2c2133a760d *man/computeGenotypeProbabilities.Rd
d7ca5b99cc8d10008a1401a1ca373abf *man/detailedPedigree-class.Rd
ec0bf5a72aee86f71fc8bf0a2e79b7e2 *man/eightParentPedigreeImproperFunnels.Rd
04bda435ee736bad12268108980c52ef *man/eightParentPedigreeRandomFunnels.Rd
d455711fa76f8f28eb78d2908a19f5ac *man/eightParentPedigreeSingleFunnel.Rd
369d3dcb68f9f455d32cb59fd5d483d4 *man/eightParentSubsetMap.Rd
1a0aff2b106188fe357a9fd44e6d87c9 *man/estimateMap.Rd
750bb01edca28fb9561f90b2a0592bdf *man/estimateMapFromImputation.Rd
521cd180bcf2069d7823cdea25539af6 *man/estimateRF.Rd
62d33c2dda41efbe8b712325ee4c22f6 *man/estimateRFSingleDesign.Rd
fc15347eddbc807162d70d90e168a459 *man/existingLocalisationStatistics.Rd
16813ef5c1fdb8b4bbb42a096ab602f6 *man/expand.Rd
ad4331fa945715d72c5744d05b9ecb02 *man/exportMapToPretzl.Rd
74d3fddfc934410988d4d62911461a14 *man/extraImputationPoints.Rd
c51e2a88ea5a87c7df9d67f6abf21c14 *man/f2Pedigree.Rd
a6b4a2610445a2e8faf0dad395658d8f *man/finalNames.Rd
a67c518eedf8283bcfaf4a7b8868bce4 *man/finals.Rd
5b4fc1f5423a93577e31823c4dfb38d6 *man/fixedNumberOfFounderAlleles.Rd
348f3b7d658f4de38fd1f25c8710229d *man/flatImputationMapNames.Rd
59672d579fca606041b4894b416938d6 *man/formGroups.Rd
c88bea1fc60656e9313852e09594c403 *man/founderNames.Rd
3f57c76b2acd7a224ff2dd18dca7cec7 *man/founders.Rd
6bd860d509488394ded06f1071665483 *man/fourParentPedigreeRandomFunnels.Rd
fe3a0c48e3d85b28e1ea99026c3a84c2 *man/fourParentPedigreeSingleFunnel.Rd
aaa53c7353e707d8a9d4ca69ef8b716e *man/fromMpMap.Rd
28fecf1e6f2a601dd0e34a47e58158f5 *man/generateGridPositions.Rd
a9f4f57ae2150021f8b4b12968e65b9f *man/generateIntervalMidPoints.Rd
ef8edca9b199b79577ffee52723c925d *man/geneticData-class.Rd
3bdbdb521e764e35a573fd683e4000e5 *man/getAllFunnels.Rd
b3a72d07f6c8e6f6d877df2c9b897351 *man/getAllFunnelsIncAIC.Rd
585c9476e2e105621683b57b95370162 *man/getChromosomes.Rd
5c88dfb6dec077a3bb2af40a559b50ca *man/getIntercrossingAndSelfingGenerations.Rd
dd7aa12523d9ad16e588b5c3c98b28c5 *man/getPositions.Rd
7ff22514dbcabf2536dc51d81c232931 *man/hetData.Rd
08c5650bc57deb25e4308d3fd50bee62 *man/hetsForSNPMarkers.Rd
abe123343b27c22ee75c09c54bec693e *man/imputationData.Rd
d03a7315e4585348b9497befe09b1dd9 *man/imputationKey.Rd
7bbf193e706b57d038aaedf0a30d41cd *man/imputationMap.Rd
a8c8b47c023eccc76d815ac56f9c77e0 *man/impute.Rd
4270a435ca000cc6f7e16585430522ac *man/imputeFounders.Rd
ed9f2d26af24730dbacd8c18ab3262d0 *man/infiniteSelfing.Rd
44a40ffd16725b409bc8fa717585bac3 *man/initialize.Rd
e355e604736f86509a38d4e83b546a9f *man/internalOperators.Rd
80fb16af7d44e416f8939799579c3cfb *man/jitterMap.Rd
ef7e91172970e0610ff738745dd71eec *man/lineNamesGeneric.Rd
c10f75c9bf68c408eb2290a620a65088 *man/lineNamesMpcross.Rd
af8a82935cde8bcecdf7bb1a12049664 *man/lineNamesPedigree.Rd
68ed37a84a61d27fd29887392157d79f *man/linesByNames.Rd
bf8bd2242de12ec2e747fe2748211fc2 *man/listCodingErrors.Rd
1f83418cfb3f5309e9b9d3f294fe7d46 *man/listCodingErrorsInfiniteSelfing.Rd
4046f2163a6f3b0a9bd57cb23bec9b9c *man/mapFunctions.Rd
1becb5341b7a38d8e87ca7bb0692685f *man/markers.Rd
f4029983ca30c4c82938dc530d976df9 *man/mpcross-class.Rd
6b44923a7511d19f93f1aa860ca7382e *man/mpcross.Rd
b20647eeca1a9add5f2b231c54b8b092 *man/mpcrossMapped-class.Rd
38dd1b5a98f32b00f1d2693fa6c0fab9 *man/mpcrossMapped.Rd
51ff8ec1e04a231ac2a25ca9c6ce3e0b *man/mpcrossRF-class.Rd
84e44755e2aa94432d1c0a53d41a2c03 *man/multiparentSNP.Rd
b77f5449915a9361bd6521037ce566c8 *man/nFounders.Rd
80469e60f15f768b629ffe823a83165d *man/nLines.Rd
b674d8889c19e5e3ba4b993aa229b5e2 *man/nMarkers.Rd
ba391386bb796f7f3ce8b0a59a30e420 *man/normalPhenotype.Rd
c690b789099ea1635051e99405481831 *man/openmp.Rd
4b4c2f5c9f6acf1b92574e6a33a15038 *man/orderCross.Rd
c3c8a3178e135faea937ae5603fa2a71 *man/pedigree-class.Rd
74e5fe01a67ff839fc1207ad2ed2dfeb *man/pedigree.Rd
1eb4720009a8e5a6c5cbbe1c8af5d4fd *man/pedigreeGraph-class.Rd
43753a96a9c4ef8d7f6e6c7bdb34bcce *man/pedigreeToGraph.Rd
3e25d03c5da17df968c54e63ab5a732f *man/plot-addExtraMarkersStatistics-ANY-method.Rd
e00392499293110debd94ba89498870a *man/plot-pedigreeGraph-ANY-method.Rd
8247cb9dcfe167c2c376ac6b083b23bf *man/plot.Rd
8a6e79e57391c1065fc62de35920ba93 *man/plotMosaic.Rd
c0a691136b56ae4f009fb70d091fcb1a *man/plotProbabilities.Rd
899ca21acc65216c997d995a8c8f5d29 *man/probabilities-class.Rd
09c4cd45ac955716aa38b15db24396bf *man/probabilityData.Rd
6b0b70d168f3884657ca82642e098d52 *man/redact.Rd
49db8177b7c87787b312d051aaf2614c *man/removeHets.Rd
015aa08de651540968306e1b1ed4e503 *man/reverseChromosomes.Rd
3097a1848b408fed257cc3f42dc186fb *man/rilPedigree.Rd
51b689a34eff0e3450444982493e62de *man/selfing.Rd
2db734d5afd3d999855660c5cc5f7d09 *man/simulateMPCross.Rd
f99b4fcdb9b27c0b4d2d72dccd0f23c0 *man/simulatedFourParentData.Rd
e07c7b2888ed65fdbc1a2c34f5f151e7 *man/sixteenParentPedigreeRandomFunnels.Rd
2041c2189e30e58ca44788ed936300ae *man/stripPedigree.Rd
6c5e7391fed9fb8c05fe428d8a17c683 *man/subset.Rd
7fc9686870694e4896b0d4e20a181fe2 *man/testDistortion.Rd
9a390e7a2d03ca904e5d477646287e31 *man/toMpMap.Rd
75aba1469386e2e63e79948642e9b41e *man/transposeProbabilities.Rd
a2487b74ea8f009ffb322b58f1de13df *man/twoParentPedigree.Rd
1b801983f85154c91bf492a7bbee9fe1 *man/wsnp_Ku_rep_c103074_89904851.Rd
400c2d6a1423e608012fc2ca16cc2027 *src/Makevars
1458624f3f7a75989f34f5c59c0c3ff3 *src/Makevars.win
b0d42696c9e869c6de0b0ed80d841930 *src/alleleDataErrors.cpp
446c00b8438b3a11b377d911ce8bac77 *src/alleleDataErrors.h
96c14cd2294ed621bdb0685f5437a378 *src/array2.h
98a9d504cfba203b21ffb094381b3615 *src/arsa.cpp
8fd9483441e99fb76c0726fe86c04cd4 *src/arsa.h
0e4f24ccb748ed0048e22040dcd39974 *src/arsaRaw.cpp
287666614d35397de99de7567e9f44e3 *src/arsaRaw.h
c345f6303f734456fc2ab271486388d1 *src/arsaRawREntryPoint.cpp
4be4404c911a2251a9f097f8f49ba8ad *src/arsaRawREntryPoint.h
f782654fc6c9c74897fc44d62a332726 *src/assignFounderPattern.cpp
e90ba7191e65514770e5c6d72fc84487 *src/assignFounderPattern.h
23fca240828e9e322e007c2adaa40c3d *src/checkHets.cpp
b8fc8a8a4d930781349adf227a53a1ca *src/checkHets.h
54519177c09c74dbe0949b91af3c51e1 *src/checkImputedBounds.cpp
32cc293dd5e6037a3cb1b00365e49dd8 *src/checkImputedBounds.h
aa505248402951cf9fb3cf7c6f8f7318 *src/combineGenotypes.cpp
a8e1a9534374f4cddf219f6568f5d4ef *src/combineGenotypes.h
f2f413c86c3eea3611c18e2879d76147 *src/combineRFDisjoint.cpp
d3e45a8fe03b4f0f2b4292dd2d056448 *src/combineRFDisjoint.h
ced0344304783eb2e2fd5f008be176d7 *src/compressedProbabilities.cpp
34e26e35e144f6f0c130a1631880801a *src/compressedProbabilities.h
1f8321e846d969d527428ab64deb888c *src/compressedProbabilities_RInterface.cpp
0f09525a35dc020cfa11200189ab00dc *src/compressedProbabilities_RInterface.h
c1dc6fe237cf2887c06706c78efc80d9 *src/computeAllEpistaticChiSquared.cpp
be68a21b423069eedfb25c7a548e7799 *src/computeAllEpistaticChiSquared.h
62dc9f8a79dedee0a9d6646e19aed72f *src/computeGenotypeProbabilities.cpp
4afb43bebb365551207bcb7009b92559 *src/computeGenotypeProbabilities.h
96602c6205e4d38927da5b50d0e80918 *src/constructLookupTable.h
e0ca82cced50d17bb3df02ba765bd8a7 *src/convertGeneticData.cpp
fb8f2430dd22c2186e5d63ba6d710a87 *src/convertGeneticData.h
45b011bfba354f3e4897917c7e167007 *src/crc32.cpp
2dde69ca9e9a480cccdf67a8630b0f96 *src/crc32.h
63d45670499781632e0f440d9c55fe83 *src/dspMatrix.cpp
226a5c46b54baefbef9a2632e024d909 *src/dspMatrix.h
380591abac050754ab54bfe7fef3d550 *src/eightParentPedigreeImproperFunnels.cpp
5694378b6ae4129d7846d8dfcd41c86f *src/eightParentPedigreeImproperFunnels.h
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